Starting phenix.real_space_refine
on Wed Sep 17 14:02:57 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8y9m_39083/09_2025/8y9m_39083.map"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.065
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     107      5.49       5
     S      27      5.16       5
     C    5430      2.51       5
     N    1614      2.21       5
     O    1960      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9138
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 853, 6897
          Classifications: {'peptide': 853}
          Link IDs: {'PTRANS': 33, 'TRANS': 819}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 1203
          Classifications: {'RNA': 56}
          Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 29, 'rna3p_pyr': 22}
          Link IDs: {'rna2p': 4, 'rna3p': 51}
    Chain: "C"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 587
          Classifications: {'DNA': 29}
          Link IDs: {'rna3p': 28}
    Chain: "D"
      Number of atoms: 451
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 451
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
  Time building chain proxies: 2.26, per 1000 atoms: 0.25
  Number of scatterers: 9138
  At special positions: 0
  Unit cell: (92.34, 104.31, 119.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      27     16.00
     P     107     15.00
     O    1960      8.00
     N    1614      7.00
     C    5430      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 245.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 7 sheets defined
      47.5% alpha, 11.7% beta
      34 base pairs and 69 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 41
      removed outlier: 4.085A  pdb=" N   SER A  37 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 72
      removed outlier: 3.721A  pdb=" N   ALA A  63 " --> pdb=" O   SER A  59 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU A  64 " --> pdb=" O   PRO A  60 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LEU A  69 " --> pdb=" O   LEU A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 89 through 99
      removed outlier: 4.386A  pdb=" N   SER A  94 " --> pdb=" O   PRO A  91 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   CYS A  95 " --> pdb=" O   SER A  92 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   TYR A  96 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   SER A  97 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A  98 " --> pdb=" O   CYS A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 121
      removed outlier: 4.402A  pdb=" N   GLY A 121 " --> pdb=" O   GLU A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 130
    Processing helix  chain 'A' and resid 139 through 143
      removed outlier: 3.538A  pdb=" N   LYS A 142 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 156 through 165
      removed outlier: 3.590A  pdb=" N   GLN A 163 " --> pdb=" O   GLU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 173
      removed outlier: 3.962A  pdb=" N   ARG A 173 " --> pdb=" O   ASN A 170 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 170 through 173'
    Processing helix  chain 'A' and resid 174 through 184
      removed outlier: 3.517A  pdb=" N   ARG A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 231
      removed outlier: 3.607A  pdb=" N   ARG A 205 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   HIS A 210 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLU A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   THR A 213 " --> pdb=" O   SER A 209 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   HIS A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 223 " --> pdb=" O   ASN A 219 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   MET A 224 " --> pdb=" O   GLN A 220 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   LYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 249
    Processing helix  chain 'A' and resid 256 through 267
      removed outlier: 4.261A  pdb=" N   VAL A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   LEU A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 284
      removed outlier: 3.858A  pdb=" N   GLN A 284 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 293
      removed outlier: 4.488A  pdb=" N   GLY A 289 " --> pdb=" O   LYS A 286 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU A 290 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU A 291 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 292 " --> pdb=" O   GLY A 289 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 312
      removed outlier: 3.507A  pdb=" N   GLU A 312 " --> pdb=" O   LYS A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
      removed outlier: 3.602A  pdb=" N   GLN A 436 " --> pdb=" O   ILE A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 453
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 512 through 534
      removed outlier: 4.015A  pdb=" N   SER A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU A 517 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LYS A 518 " --> pdb=" O   LEU A 514 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG A 519 " --> pdb=" O   ILE A 515 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ILE A 521 " --> pdb=" O   LEU A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 551
      removed outlier: 3.951A  pdb=" N   GLU A 551 " --> pdb=" O   THR A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 575
      removed outlier: 3.533A  pdb=" N   GLN A 564 " --> pdb=" O   ARG A 560 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ALA A 568 " --> pdb=" O   GLN A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 583
      removed outlier: 3.830A  pdb=" N   TYR A 579 " --> pdb=" O   ASN A 575 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   MET A 581 " --> pdb=" O   PHE A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 610
      removed outlier: 4.113A  pdb=" N   ARG A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU A 596 " --> pdb=" O   ALA A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 633 through 649
      removed outlier: 3.791A  pdb=" N   LEU A 637 " --> pdb=" O   PHE A 633 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ARG A 639 " --> pdb=" O   ASP A 635 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   VAL A 641 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA A 642 " --> pdb=" O   ARG A 638 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A 648 " --> pdb=" O   THR A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 678
      removed outlier: 3.577A  pdb=" N   VAL A 674 " --> pdb=" O   ASN A 670 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   LEU A 676 " --> pdb=" O   ALA A 672 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU A 677 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 692
      removed outlier: 3.660A  pdb=" N   LEU A 684 " --> pdb=" O   ARG A 680 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A 687 " --> pdb=" O   LEU A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 739 through 753
    Processing helix  chain 'A' and resid 782 through 790
    Processing helix  chain 'A' and resid 830 through 846
    Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 8
      removed outlier: 4.331A  pdb=" N   SER A 429 " --> pdb=" O   GLU A 404 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   GLU A 404 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   HIS A 379 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ALA A 371 " --> pdb=" O   HIS A 379 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LYS A 381 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   LEU A 369 " --> pdb=" O   LYS A 381 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 331
      removed outlier: 5.409A  pdb=" N   PHE A 420 " --> pdb=" O   ILE A  14 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   PHE A 359 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   TYR A  17 " --> pdb=" O   LYS A 357 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   LYS A 357 " --> pdb=" O   TYR A  17 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL A 349 " --> pdb=" O   GLU A 342 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 48
    Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 489
      removed outlier: 4.549A  pdb=" N   TYR A 494 " --> pdb=" O   GLY A 480 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLY A 480 " --> pdb=" O   TYR A 494 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE A 498 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   LYS A 476 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   VAL A 461 " --> pdb=" O   ALA A 477 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   GLY A 462 " --> pdb=" O   PHE A 656 " (cutoff:3.500A)
      removed outlier: 8.920A  pdb=" N   GLU A 658 " --> pdb=" O   GLY A 462 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   VAL A 655 " --> pdb=" O   VAL A 698 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   VAL A 700 " --> pdb=" O   VAL A 655 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   PHE A 657 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 717 through 718
      removed outlier: 4.011A  pdb=" N   ILE A 726 " --> pdb=" O   MET A 737 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG A 852 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 762
    Processing sheet with id=AA7, first strand: chain 'A' and resid 796 through 800
      removed outlier: 3.740A  pdb=" N   LEU A 798 " --> pdb=" O   THR A 806 " (cutoff:3.500A)

    297 hydrogen bonds defined for protein.
    810 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      84 hydrogen bonds
      160 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      69 stacking parallelities
  Total time for adding SS restraints: 2.11

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.33: 1806
        1.33 -     1.45: 2706
        1.45 -     1.57: 4785
        1.57 -     1.69: 210
        1.69 -     1.81: 43
  Bond restraints: 9550
  Sorted by residual:
  bond pdb=" O3'  DG D  11 "
       pdb=" P    DT D  12 "
    ideal  model  delta    sigma   weight residual
    1.607  1.510  0.097 1.50e-02 4.44e+03 4.14e+01
  bond pdb=" O3'  DC C -20 "
       pdb=" P    DT C -19 "
    ideal  model  delta    sigma   weight residual
    1.607  1.570  0.037 1.50e-02 4.44e+03 5.95e+00
  bond pdb=" N   THR A 763 "
       pdb=" CA  THR A 763 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.28e-02 6.10e+03 5.55e+00
  bond pdb=" C   VAL A 762 "
       pdb=" O   VAL A 762 "
    ideal  model  delta    sigma   weight residual
    1.238  1.214  0.024 1.10e-02 8.26e+03 4.68e+00
  bond pdb=" O3'  DT C -19 "
       pdb=" P    DA C -18 "
    ideal  model  delta    sigma   weight residual
    1.607  1.637 -0.030 1.50e-02 4.44e+03 4.07e+00
  ... (remaining 9545 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.88: 13220
        2.88 -     5.77: 138
        5.77 -     8.65: 11
        8.65 -    11.53: 0
       11.53 -    14.42: 1
  Bond angle restraints: 13370
  Sorted by residual:
  angle pdb=" O3'  DT C -19 "
        pdb=" C3'  DT C -19 "
        pdb=" C2'  DT C -19 "
      ideal   model   delta    sigma   weight residual
     111.50   97.08   14.42 1.50e+00 4.44e-01 9.24e+01
  angle pdb=" N   ILE A 432 "
        pdb=" CA  ILE A 432 "
        pdb=" C   ILE A 432 "
      ideal   model   delta    sigma   weight residual
     111.91  105.97    5.94 8.90e-01 1.26e+00 4.46e+01
  angle pdb=" O2'   A B  19 "
        pdb=" C2'   A B  19 "
        pdb=" C1'   A B  19 "
      ideal   model   delta    sigma   weight residual
     108.40  100.58    7.82 1.50e+00 4.44e-01 2.72e+01
  angle pdb=" O2'   G B  20 "
        pdb=" C2'   G B  20 "
        pdb=" C1'   G B  20 "
      ideal   model   delta    sigma   weight residual
     111.80  118.88   -7.08 1.50e+00 4.44e-01 2.23e+01
  angle pdb=" C3'  DT C -19 "
        pdb=" C2'  DT C -19 "
        pdb=" C1'  DT C -19 "
      ideal   model   delta    sigma   weight residual
     101.60  108.32   -6.72 1.50e+00 4.44e-01 2.01e+01
  ... (remaining 13365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.04: 5273
       32.04 -    64.08: 407
       64.08 -    96.11: 35
       96.11 -   128.15: 2
      128.15 -   160.19: 1
  Dihedral angle restraints: 5718
    sinusoidal: 3231
      harmonic: 2487
  Sorted by residual:
  dihedral pdb=" O4'   U B -18 "
           pdb=" C1'   U B -18 "
           pdb=" N1    U B -18 "
           pdb=" C2    U B -18 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   39.81  160.19     1      1.50e+01 4.44e-03 8.28e+01
  dihedral pdb=" C5'   G B  20 "
           pdb=" C4'   G B  20 "
           pdb=" C3'   G B  20 "
           pdb=" O3'   G B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  111.27   35.73     1      8.00e+00 1.56e-02 2.82e+01
  dihedral pdb=" O4'   G B  20 "
           pdb=" C4'   G B  20 "
           pdb=" C3'   G B  20 "
           pdb=" C2'   G B  20 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -10.06   34.06     1      8.00e+00 1.56e-02 2.57e+01
  ... (remaining 5715 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.087: 1422
       0.087 -    0.175: 78
       0.175 -    0.262: 1
       0.262 -    0.350: 1
       0.350 -    0.437: 1
  Chirality restraints: 1503
  Sorted by residual:
  chirality pdb=" C2'   G B  20 "
            pdb=" C3'   G B  20 "
            pdb=" O2'   G B  20 "
            pdb=" C1'   G B  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.08   -0.44 2.00e-01 2.50e+01 4.78e+00
  chirality pdb=" CA  VAL A 762 "
            pdb=" N   VAL A 762 "
            pdb=" C   VAL A 762 "
            pdb=" CB  VAL A 762 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CB  VAL A 762 "
            pdb=" CA  VAL A 762 "
            pdb=" CG1 VAL A 762 "
            pdb=" CG2 VAL A 762 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1500 not shown)

  Planarity restraints: 1325
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT C -19 "    0.043 2.00e-02 2.50e+03   2.58e-02 1.66e+01
        pdb=" N1   DT C -19 "   -0.068 2.00e-02 2.50e+03
        pdb=" C2   DT C -19 "    0.003 2.00e-02 2.50e+03
        pdb=" O2   DT C -19 "    0.001 2.00e-02 2.50e+03
        pdb=" N3   DT C -19 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DT C -19 "    0.002 2.00e-02 2.50e+03
        pdb=" O4   DT C -19 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DT C -19 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT C -19 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DT C -19 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  20 "   -0.053 2.00e-02 2.50e+03   2.30e-02 1.58e+01
        pdb=" N9    G B  20 "    0.052 2.00e-02 2.50e+03
        pdb=" C8    G B  20 "    0.007 2.00e-02 2.50e+03
        pdb=" N7    G B  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" C5    G B  20 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    G B  20 "   -0.022 2.00e-02 2.50e+03
        pdb=" O6    G B  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" N1    G B  20 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2    G B  20 "    0.004 2.00e-02 2.50e+03
        pdb=" N2    G B  20 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  20 "    0.010 2.00e-02 2.50e+03
        pdb=" C4    G B  20 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  19 "   -0.029 2.00e-02 2.50e+03   1.40e-02 5.42e+00
        pdb=" N9    A B  19 "    0.032 2.00e-02 2.50e+03
        pdb=" C8    A B  19 "    0.002 2.00e-02 2.50e+03
        pdb=" N7    A B  19 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5    A B  19 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A B  19 "   -0.005 2.00e-02 2.50e+03
        pdb=" N6    A B  19 "   -0.002 2.00e-02 2.50e+03
        pdb=" N1    A B  19 "   -0.007 2.00e-02 2.50e+03
        pdb=" C2    A B  19 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A B  19 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A B  19 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1322 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 499
        2.71 -     3.26: 8391
        3.26 -     3.81: 14785
        3.81 -     4.35: 18699
        4.35 -     4.90: 29600
  Nonbonded interactions: 71974
  Sorted by model distance:
  nonbonded pdb=" O   ALA A 445 "
            pdb=" NH1 ARG A 784 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OH  TYR A 365 "
            pdb=" OH  TYR A 426 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O2'   C B -19 "
            pdb=" OP2   A B -17 "
     model   vdw
     2.189 3.040
  nonbonded pdb=" NH2 ARG A 634 "
            pdb=" O   LEU A 676 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" O   TYR A 586 "
            pdb=" NH2 ARG A 640 "
     model   vdw
     2.193 3.120
  ... (remaining 71969 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     11.020
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.097   9550  Z= 0.232
  Angle     :  0.754  14.418  13370  Z= 0.453
  Chirality :  0.045   0.437   1503
  Planarity :  0.005   0.051   1325
  Dihedral  : 19.546 160.188   4118
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  0.81 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.28), residues: 847
  helix: -0.41 (0.27), residues: 361
  sheet: -0.47 (0.47), residues: 119
  loop : -1.40 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 440 
 TYR   0.025   0.002   TYR A 778 
 PHE   0.014   0.002   PHE A 242 
 TRP   0.021   0.002   TRP A 259 
 HIS   0.007   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00467 ( 9550)
  covalent geometry    : angle       0.75426 (13370)
  hydrogen bonds       : bond        0.20685 (  381)
  hydrogen bonds       : angle       6.76614 (  970)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 112
  average time/residue: 0.7208
  time to fit residues: 85.3698
Evaluate side-chains
  75 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  777 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.2164

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.181737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.136708 restraints weight = 12024.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.66
r_work: 0.3637 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.1176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9550  Z= 0.155
  Angle     :  0.607   7.825  13370  Z= 0.326
  Chirality :  0.039   0.203   1503
  Planarity :  0.004   0.046   1325
  Dihedral  : 21.187 161.660   2384
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 10.80 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.28), residues: 847
  helix:  0.12 (0.27), residues: 375
  sheet: -0.26 (0.46), residues: 133
  loop : -1.20 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  67 
 TYR   0.015   0.001   TYR A 822 
 PHE   0.013   0.001   PHE A 531 
 TRP   0.012   0.002   TRP A 548 
 HIS   0.009   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9550)
  covalent geometry    : angle       0.60743 (13370)
  hydrogen bonds       : bond        0.05269 (  381)
  hydrogen bonds       : angle       4.51332 (  970)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A  291 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7420 (mm)
REVERT: A  404 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: A  498 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7254 (pt)
REVERT: A  572 ARG cc_start: 0.7193 (mtm110) cc_final: 0.6977 (ptt90)
REVERT: A  581 MET cc_start: 0.6840 (tmt) cc_final: 0.6632 (tmt)
REVERT: A  697 MET cc_start: 0.8692 (ttp) cc_final: 0.8418 (ttp)
REVERT: A  738 ASP cc_start: 0.7960 (t0) cc_final: 0.7627 (t0)
REVERT: A  787 LYS cc_start: 0.6145 (mttp) cc_final: 0.5702 (mmtm)
REVERT: A  848 GLU cc_start: 0.8533 (mp0) cc_final: 0.8133 (mp0)
  outliers start: 17
  outliers final: 9
  residues processed: 90
  average time/residue: 0.6337
  time to fit residues: 60.8021
Evaluate side-chains
  82 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  242 PHE
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  850 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 14 optimal weight:   20.0000
   chunk 0 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 34 optimal weight:    0.4980
   chunk 77 optimal weight:    0.6980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 754 HIS
A 834 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.182158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136772 restraints weight = 11916.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3760 rms_B_bonded: 2.68
r_work: 0.3641 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   9550  Z= 0.145
  Angle     :  0.564   6.094  13370  Z= 0.305
  Chirality :  0.038   0.177   1503
  Planarity :  0.004   0.034   1325
  Dihedral  : 21.049 160.698   2382
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 6.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.23 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.29), residues: 847
  helix:  0.28 (0.27), residues: 376
  sheet:  0.01 (0.46), residues: 131
  loop : -1.19 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  41 
 TYR   0.013   0.001   TYR A 822 
 PHE   0.012   0.001   PHE A 531 
 TRP   0.011   0.001   TRP A  24 
 HIS   0.008   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9550)
  covalent geometry    : angle       0.56436 (13370)
  hydrogen bonds       : bond        0.04704 (  381)
  hydrogen bonds       : angle       4.14651 (  970)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 74
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  291 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7424 (mm)
REVERT: A  404 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: A  498 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7212 (pt)
REVERT: A  562 MET cc_start: 0.5256 (mtt) cc_final: 0.5037 (mtp)
REVERT: A  572 ARG cc_start: 0.7148 (mtm110) cc_final: 0.6941 (ptt90)
REVERT: A  697 MET cc_start: 0.8686 (ttp) cc_final: 0.8452 (ttp)
REVERT: A  787 LYS cc_start: 0.6167 (mttp) cc_final: 0.5690 (mmtm)
REVERT: A  848 GLU cc_start: 0.8558 (mp0) cc_final: 0.8205 (mp0)
  outliers start: 28
  outliers final: 11
  residues processed: 86
  average time/residue: 0.6464
  time to fit residues: 59.3319
Evaluate side-chains
  81 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  850 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 80 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 93 optimal weight:   10.0000
   chunk 61 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 66 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    3.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 754 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.175434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130049 restraints weight = 12379.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 2.69
r_work: 0.3538 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9550  Z= 0.274
  Angle     :  0.684   7.423  13370  Z= 0.363
  Chirality :  0.044   0.186   1503
  Planarity :  0.005   0.051   1325
  Dihedral  : 21.180 165.493   2382
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 15.38 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.94 (0.28), residues: 847
  helix: -0.10 (0.27), residues: 377
  sheet: -0.12 (0.46), residues: 129
  loop : -1.31 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 836 
 TYR   0.026   0.002   TYR A 217 
 PHE   0.021   0.002   PHE A 531 
 TRP   0.015   0.002   TRP A 323 
 HIS   0.005   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 ( 9550)
  covalent geometry    : angle       0.68385 (13370)
  hydrogen bonds       : bond        0.06386 (  381)
  hydrogen bonds       : angle       4.38202 (  970)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 65
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8326 (mt-10)
REVERT: A  562 MET cc_start: 0.5301 (mtt) cc_final: 0.5066 (mtp)
REVERT: A  581 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6551 (tmt)
REVERT: A  607 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7283 (tt0)
REVERT: A  787 LYS cc_start: 0.6409 (mttp) cc_final: 0.5951 (mmtp)
REVERT: A  846 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7700 (mp0)
REVERT: A  848 GLU cc_start: 0.8572 (mp0) cc_final: 0.8198 (mp0)
  outliers start: 30
  outliers final: 13
  residues processed: 83
  average time/residue: 0.7084
  time to fit residues: 62.3642
Evaluate side-chains
  77 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  581 MET
Chi-restraints excluded: chain A residue  607 GLU
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  846 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    9.9990
   chunk 60 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 564 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.177659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.132462 restraints weight = 12368.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.69
r_work: 0.3567 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9550  Z= 0.191
  Angle     :  0.607   7.525  13370  Z= 0.326
  Chirality :  0.040   0.193   1503
  Planarity :  0.004   0.038   1325
  Dihedral  : 21.101 166.281   2382
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 16.87 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.28), residues: 847
  helix:  0.06 (0.27), residues: 378
  sheet: -0.11 (0.46), residues: 129
  loop : -1.28 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  68 
 TYR   0.018   0.001   TYR A 217 
 PHE   0.019   0.002   PHE A 242 
 TRP   0.014   0.001   TRP A 323 
 HIS   0.005   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 9550)
  covalent geometry    : angle       0.60661 (13370)
  hydrogen bonds       : bond        0.05286 (  381)
  hydrogen bonds       : angle       4.14194 (  970)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 64
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7240 (mp)
REVERT: A  404 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8327 (mt-10)
REVERT: A  562 MET cc_start: 0.5303 (mtt) cc_final: 0.5077 (mtp)
REVERT: A  738 ASP cc_start: 0.7703 (t0) cc_final: 0.6946 (t0)
REVERT: A  787 LYS cc_start: 0.6350 (mttp) cc_final: 0.5886 (mmtp)
REVERT: A  846 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7521 (mp0)
REVERT: A  848 GLU cc_start: 0.8577 (mp0) cc_final: 0.8180 (mp0)
  outliers start: 31
  outliers final: 14
  residues processed: 84
  average time/residue: 0.6676
  time to fit residues: 59.5614
Evaluate side-chains
  77 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 VAL
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  846 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 78 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9990
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.181004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135974 restraints weight = 12322.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.71
r_work: 0.3609 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9550  Z= 0.138
  Angle     :  0.546   7.549  13370  Z= 0.297
  Chirality :  0.037   0.178   1503
  Planarity :  0.004   0.037   1325
  Dihedral  : 20.983 163.664   2382
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 17.14 %
    Favored  : 78.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.29), residues: 847
  helix:  0.39 (0.28), residues: 376
  sheet:  0.01 (0.46), residues: 129
  loop : -1.09 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  68 
 TYR   0.013   0.001   TYR A 822 
 PHE   0.021   0.001   PHE A 242 
 TRP   0.011   0.001   TRP A  24 
 HIS   0.005   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9550)
  covalent geometry    : angle       0.54626 (13370)
  hydrogen bonds       : bond        0.04268 (  381)
  hydrogen bonds       : angle       3.82032 (  970)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 69
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  404 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: A  436 GLN cc_start: 0.6880 (mm110) cc_final: 0.6534 (mm-40)
REVERT: A  498 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7247 (pt)
REVERT: A  572 ARG cc_start: 0.7319 (mtm110) cc_final: 0.6502 (ttp-110)
REVERT: A  787 LYS cc_start: 0.6162 (mttp) cc_final: 0.5737 (mmtm)
REVERT: A  846 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7684 (mp0)
REVERT: A  848 GLU cc_start: 0.8609 (mp0) cc_final: 0.8295 (mp0)
  outliers start: 32
  outliers final: 13
  residues processed: 89
  average time/residue: 0.6457
  time to fit residues: 61.3474
Evaluate side-chains
  81 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  850 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 55 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 78 optimal weight:    4.9990
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.176694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131456 restraints weight = 12310.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3675 rms_B_bonded: 2.69
r_work: 0.3557 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9550  Z= 0.232
  Angle     :  0.634   7.937  13370  Z= 0.338
  Chirality :  0.042   0.191   1503
  Planarity :  0.004   0.041   1325
  Dihedral  : 21.088 165.341   2382
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 17.95 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.62 (0.29), residues: 847
  helix:  0.21 (0.27), residues: 377
  sheet: -0.02 (0.46), residues: 129
  loop : -1.19 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 566 
 TYR   0.021   0.002   TYR A 217 
 PHE   0.024   0.002   PHE A 242 
 TRP   0.013   0.002   TRP A 323 
 HIS   0.007   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 ( 9550)
  covalent geometry    : angle       0.63411 (13370)
  hydrogen bonds       : bond        0.05650 (  381)
  hydrogen bonds       : angle       4.11365 (  970)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 66
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 MET cc_start: 0.2560 (OUTLIER) cc_final: 0.1651 (tmm)
REVERT: A  291 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: A  399 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8644 (mm)
REVERT: A  404 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8331 (mt-10)
REVERT: A  442 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7215 (m-10)
REVERT: A  551 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6925 (pt0)
REVERT: A  737 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8097 (mtp)
REVERT: A  738 ASP cc_start: 0.8159 (t0) cc_final: 0.7485 (t0)
REVERT: A  787 LYS cc_start: 0.6410 (mttp) cc_final: 0.5883 (mmtm)
REVERT: A  845 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.7729 (p)
REVERT: A  846 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7620 (mp0)
REVERT: A  848 GLU cc_start: 0.8608 (mp0) cc_final: 0.8217 (mp0)
  outliers start: 33
  outliers final: 15
  residues processed: 87
  average time/residue: 0.6461
  time to fit residues: 59.9062
Evaluate side-chains
  84 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 61
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  120 GLU
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  291 LEU
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  342 GLU
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  442 PHE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  551 GLU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  846 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    0.0010
   chunk 54 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 90 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.5192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.178953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133111 restraints weight = 12247.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 2.77
r_work: 0.3558 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9550  Z= 0.162
  Angle     :  0.587   9.292  13370  Z= 0.313
  Chirality :  0.039   0.185   1503
  Planarity :  0.004   0.038   1325
  Dihedral  : 21.008 164.742   2382
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.95 %
    Favored  : 77.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.29), residues: 847
  helix:  0.39 (0.27), residues: 378
  sheet:  0.05 (0.46), residues: 129
  loop : -1.16 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.015   0.001   TYR A 217 
 PHE   0.020   0.001   PHE A 242 
 TRP   0.012   0.001   TRP A 323 
 HIS   0.006   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9550)
  covalent geometry    : angle       0.58667 (13370)
  hydrogen bonds       : bond        0.04751 (  381)
  hydrogen bonds       : angle       3.97473 (  970)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 62
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  125 MET cc_start: 0.2486 (OUTLIER) cc_final: 0.1330 (tmm)
REVERT: A  246 LEU cc_start: 0.3117 (mt) cc_final: 0.2914 (mt)
REVERT: A  399 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8612 (mm)
REVERT: A  404 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8272 (mt-10)
REVERT: A  442 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7135 (m-10)
REVERT: A  551 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6854 (pt0)
REVERT: A  562 MET cc_start: 0.5601 (mtp) cc_final: 0.5338 (mtp)
REVERT: A  721 GLN cc_start: 0.9087 (mt0) cc_final: 0.8873 (mp10)
REVERT: A  737 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7825 (mtp)
REVERT: A  738 ASP cc_start: 0.8048 (t0) cc_final: 0.7388 (t0)
REVERT: A  787 LYS cc_start: 0.6336 (mttp) cc_final: 0.5804 (mmtm)
REVERT: A  845 VAL cc_start: 0.8310 (OUTLIER) cc_final: 0.7801 (p)
REVERT: A  846 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7686 (mp0)
REVERT: A  848 GLU cc_start: 0.8629 (mp0) cc_final: 0.8294 (mp0)
REVERT: A  861 ILE cc_start: 0.7347 (OUTLIER) cc_final: 0.7131 (mt)
  outliers start: 35
  outliers final: 14
  residues processed: 84
  average time/residue: 0.5955
  time to fit residues: 53.5180
Evaluate side-chains
  85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  442 PHE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  551 GLU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  737 MET
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  861 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 31 optimal weight:    0.3980
   chunk 84 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 27 optimal weight:    9.9990
   chunk 89 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 81 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.178577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133277 restraints weight = 12298.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 2.71
r_work: 0.3574 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9550  Z= 0.180
  Angle     :  0.612   9.003  13370  Z= 0.325
  Chirality :  0.039   0.178   1503
  Planarity :  0.004   0.038   1325
  Dihedral  : 21.000 164.448   2382
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 19.16 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.29), residues: 847
  helix:  0.36 (0.28), residues: 377
  sheet:  0.04 (0.46), residues: 129
  loop : -1.18 (0.32), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 836 
 TYR   0.017   0.001   TYR A 217 
 PHE   0.024   0.002   PHE A 242 
 TRP   0.012   0.001   TRP A 323 
 HIS   0.006   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 9550)
  covalent geometry    : angle       0.61198 (13370)
  hydrogen bonds       : bond        0.05029 (  381)
  hydrogen bonds       : angle       4.04130 (  970)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 69
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  125 MET cc_start: 0.2462 (OUTLIER) cc_final: 0.1301 (tmm)
REVERT: A  246 LEU cc_start: 0.3120 (mt) cc_final: 0.2911 (mt)
REVERT: A  391 ARG cc_start: 0.8315 (mmp-170) cc_final: 0.7912 (tpp-160)
REVERT: A  399 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8604 (mm)
REVERT: A  404 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: A  436 GLN cc_start: 0.6780 (mm110) cc_final: 0.6380 (mm-40)
REVERT: A  442 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7191 (m-10)
REVERT: A  551 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6854 (pt0)
REVERT: A  562 MET cc_start: 0.5610 (mtp) cc_final: 0.5314 (mtp)
REVERT: A  721 GLN cc_start: 0.9114 (mt0) cc_final: 0.8914 (mp10)
REVERT: A  738 ASP cc_start: 0.8128 (t0) cc_final: 0.7485 (t0)
REVERT: A  787 LYS cc_start: 0.6370 (mttp) cc_final: 0.5829 (mmtm)
REVERT: A  845 VAL cc_start: 0.8328 (OUTLIER) cc_final: 0.7779 (p)
REVERT: A  846 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7662 (mp0)
REVERT: A  848 GLU cc_start: 0.8628 (mp0) cc_final: 0.8295 (mp0)
  outliers start: 25
  outliers final: 15
  residues processed: 84
  average time/residue: 0.6795
  time to fit residues: 60.7837
Evaluate side-chains
  85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 64
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  442 PHE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  551 GLU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  856 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 85 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.178020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.132620 restraints weight = 12373.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 2.72
r_work: 0.3559 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
moved from start:          0.2170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9550  Z= 0.193
  Angle     :  0.628   9.884  13370  Z= 0.332
  Chirality :  0.040   0.183   1503
  Planarity :  0.004   0.038   1325
  Dihedral  : 21.003 164.883   2382
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 19.84 %
    Favored  : 77.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.29), residues: 847
  helix:  0.34 (0.27), residues: 376
  sheet:  0.02 (0.46), residues: 129
  loop : -1.22 (0.32), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 560 
 TYR   0.019   0.001   TYR A 217 
 PHE   0.024   0.002   PHE A 242 
 TRP   0.013   0.002   TRP A 323 
 HIS   0.006   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9550)
  covalent geometry    : angle       0.62812 (13370)
  hydrogen bonds       : bond        0.05221 (  381)
  hydrogen bonds       : angle       4.07151 (  970)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1694 Ramachandran restraints generated.
    847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 64
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  125 MET cc_start: 0.2489 (OUTLIER) cc_final: 0.1397 (tmm)
REVERT: A  246 LEU cc_start: 0.3069 (mt) cc_final: 0.2859 (mt)
REVERT: A  391 ARG cc_start: 0.8327 (mmp-170) cc_final: 0.7929 (tpp-160)
REVERT: A  399 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8607 (mm)
REVERT: A  404 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: A  436 GLN cc_start: 0.6846 (mm110) cc_final: 0.6424 (mm-40)
REVERT: A  442 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7209 (m-10)
REVERT: A  551 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6846 (pt0)
REVERT: A  562 MET cc_start: 0.5646 (mtp) cc_final: 0.5343 (mtp)
REVERT: A  721 GLN cc_start: 0.9099 (mt0) cc_final: 0.8875 (mp10)
REVERT: A  738 ASP cc_start: 0.8142 (t0) cc_final: 0.7471 (t0)
REVERT: A  787 LYS cc_start: 0.6341 (mttp) cc_final: 0.5824 (mmtm)
REVERT: A  845 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7805 (p)
REVERT: A  846 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7649 (mp0)
REVERT: A  848 GLU cc_start: 0.8622 (mp0) cc_final: 0.8286 (mp0)
  outliers start: 23
  outliers final: 16
  residues processed: 79
  average time/residue: 0.6755
  time to fit residues: 56.7223
Evaluate side-chains
  85 residues out of total 741 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   11 LEU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  125 MET
Chi-restraints excluded: chain A residue  175 LEU
Chi-restraints excluded: chain A residue  216 GLU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  331 VAL
Chi-restraints excluded: chain A residue  399 ILE
Chi-restraints excluded: chain A residue  442 PHE
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  551 GLU
Chi-restraints excluded: chain A residue  595 LEU
Chi-restraints excluded: chain A residue  764 LYS
Chi-restraints excluded: chain A residue  805 VAL
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  846 GLU
Chi-restraints excluded: chain A residue  850 LEU
Chi-restraints excluded: chain A residue  856 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 13 optimal weight:   20.0000
   chunk 44 optimal weight:    4.9990
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 75 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.181554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135962 restraints weight = 12291.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 2.75
r_work: 0.3606 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9550  Z= 0.129
  Angle     :  0.566  10.007  13370  Z= 0.301
  Chirality :  0.037   0.172   1503
  Planarity :  0.004   0.037   1325
  Dihedral  : 20.835 161.499   2382
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.38 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.20 (0.29), residues: 847
  helix:  0.66 (0.28), residues: 373
  sheet:  0.13 (0.46), residues: 129
  loop : -1.05 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 394 
 TYR   0.012   0.001   TYR A 217 
 PHE   0.019   0.001   PHE A 242 
 TRP   0.014   0.001   TRP A 548 
 HIS   0.005   0.001   HIS A 643 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9550)
  covalent geometry    : angle       0.56617 (13370)
  hydrogen bonds       : bond        0.04082 (  381)
  hydrogen bonds       : angle       3.84006 (  970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3187.99 seconds
wall clock time: 55 minutes 8.34 seconds (3308.34 seconds total)